Queen.pm 31.7 KB
Newer Older
Jessica Severin's avatar
Jessica Severin committed
1 2 3 4 5 6
#
# You may distribute this module under the same terms as perl itself

=pod 

=head1 NAME
7

8
  Bio::EnsEMBL::Hive::Queen
Jessica Severin's avatar
Jessica Severin committed
9 10

=head1 SYNOPSIS
11

12
  The Queen of the Hive based job control system
Jessica Severin's avatar
Jessica Severin committed
13 14

=head1 DESCRIPTION
15

16 17 18 19 20 21 22 23 24 25 26 27
  The Queen of the Hive based job control system is responsible to 'birthing' the
  correct number of workers of the right type so that they can find jobs to do.
  It will also free up jobs of Workers that died unexpectantly so that other workers
  can claim them to do.

  Hive based processing is a concept based on a more controlled version
  of an autonomous agent type system.  Each worker is not told what to do
  (like a centralized control system - like the current pipeline system)
  but rather queries a central database for jobs (give me jobs).

  Each worker is linked to an analysis_id, registers its self on creation
  into the Hive, creates a RunnableDB instance of the Analysis->module,
28
  gets $worker->batch_size() jobs from the analysis_job table, does its
29
  work, creates the next layer of analysis_job entries by interfacing to
30 31 32
  the DataflowRuleAdaptor to determine the analyses it needs to pass its
  output data to and creates jobs on the next analysis database.
  It repeats this cycle until it has lived its lifetime or until there are no
33 34 35 36 37 38 39 40 41 42
  more jobs left.
  The lifetime limit is just a safety limit to prevent these from 'infecting'
  a system.

  The Queens job is to simply birth Workers of the correct analysis_id to get the
  work down.  The only other thing the Queen does is free up jobs that were
  claimed by Workers that died unexpectantly so that other workers can take
  over the work.

  The Beekeeper is in charge of interfacing between the Queen and a compute resource
43
  or 'compute farm'.  Its job is to query Queens if they need any workers and to
44 45 46
  send the requested number of workers to open machines via the runWorker.pl script.
  It is also responsible for interfacing with the Queen to identify worker which died
  unexpectantly.
Jessica Severin's avatar
Jessica Severin committed
47 48

=head1 CONTACT
49

50
  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
Jessica Severin's avatar
Jessica Severin committed
51 52

=head1 APPENDIX
53

54 55
  The rest of the documentation details each of the object methods. 
  Internal methods are usually preceded with a _
Jessica Severin's avatar
Jessica Severin committed
56 57 58

=cut

59

Jessica Severin's avatar
Jessica Severin committed
60 61 62
package Bio::EnsEMBL::Hive::Queen;

use strict;
63
use POSIX;
Leo Gordon's avatar
Leo Gordon committed
64
use Sys::Hostname;
65 66 67
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;

Jessica Severin's avatar
Jessica Severin committed
68
use Bio::EnsEMBL::Hive::Worker;
69
use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
Jessica Severin's avatar
Jessica Severin committed
70

Leo Gordon's avatar
Leo Gordon committed
71
use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
72

Jessica Severin's avatar
Jessica Severin committed
73

74
############################
Jessica Severin's avatar
Jessica Severin committed
75
#
76
# PUBLIC API for Workers
Jessica Severin's avatar
Jessica Severin committed
77
#
78
############################
Jessica Severin's avatar
Jessica Severin committed
79 80 81

=head2 create_new_worker

82
  Arg [1]    : $analysis_id (optional)
Jessica Severin's avatar
Jessica Severin committed
83
  Example    :
84 85 86 87 88 89
  Description: If analysis_id is specified it will try to create a worker based
               on that analysis.  If not specified the queen will analyze the hive
               and pick the analysis that has the most amount of work to be done.
               It creates an entry in the hive table, and returns a Worker object 
               based on that insert.  This guarantees that each worker registered
               in this queens hive is properly registered.
Jessica Severin's avatar
Jessica Severin committed
90 91 92 93 94 95 96
  Returntype : Bio::EnsEMBL::Hive::Worker
  Exceptions :
  Caller     :

=cut

sub create_new_worker {
97 98
  my ($self, @args) = @_;

Leo Gordon's avatar
Leo Gordon committed
99 100
  my ($rc_id, $analysis_id, $beekeeper ,$pid, $job, $no_write) =
     rearrange([qw(rc_id analysis_id beekeeper process_id job no_write) ], @args);
Jessica Severin's avatar
Jessica Severin committed
101

102
  my $analStatsDBA = $self->db->get_AnalysisStatsAdaptor;
103
  return undef unless($analStatsDBA);
104

105
  $analysis_id = $job->analysis_id if(defined($job));
106
  
107 108 109
  my $analysisStats;
  if($analysis_id) {
    $analysisStats = $analStatsDBA->fetch_by_analysis_id($analysis_id);
110
    $self->safe_synchronize_AnalysisStats($analysisStats);
111
    #return undef unless(($analysisStats->status ne 'BLOCKED') and ($analysisStats->num_required_workers > 0));
112
  } else {
Leo Gordon's avatar
Leo Gordon committed
113
    $analysisStats = $self->_pick_best_analysis_for_new_worker($rc_id);
114
  }
115
  return undef unless($analysisStats);
116

117 118
  unless($job) {
    #go into autonomous mode
119
    return undef if($self->get_hive_current_load() >= 1.1);
120
    
121 122
    $analStatsDBA->decrease_needed_workers($analysisStats->analysis_id);
    $analStatsDBA->increase_running_workers($analysisStats->analysis_id);
123 124 125 126 127 128 129 130 131 132
    $analysisStats->print_stats;
    
    if($analysisStats->status eq 'BLOCKED') {
      print("Analysis is BLOCKED, can't create workers\n");
      return undef;
    }
    if($analysisStats->status eq 'DONE') {
      print("Analysis is DONE, don't need to create workers\n");
      return undef;
    }
133
  }
134
  
Jessica Severin's avatar
Jessica Severin committed
135
  my $host = hostname;
136
  $pid = $$ unless($pid);
137
  $beekeeper = '' unless($beekeeper);
Jessica Severin's avatar
Jessica Severin committed
138

139 140 141
  my $sql = q{INSERT INTO hive 
              (born, last_check_in, process_id, analysis_id, beekeeper, host)
              VALUES (NOW(), NOW(), ?,?,?,?)};
Jessica Severin's avatar
Jessica Severin committed
142 143

  my $sth = $self->prepare($sql);
144
  $sth->execute($pid, $analysisStats->analysis_id, $beekeeper, $host);
Leo Gordon's avatar
Leo Gordon committed
145
  my $worker_id = $sth->{'mysql_insertid'};
Jessica Severin's avatar
Jessica Severin committed
146 147
  $sth->finish;

Leo Gordon's avatar
Leo Gordon committed
148
  my $worker = $self->fetch_by_worker_id($worker_id);
Jessica Severin's avatar
Jessica Severin committed
149 150
  $worker=undef unless($worker and $worker->analysis);

151
  if($worker and $analysisStats) {
152
    $analysisStats->update_status('WORKING');
Jessica Severin's avatar
Jessica Severin committed
153
  }
154 155 156 157
  
  $worker->_specific_job($job) if(defined($job));
  $worker->execute_writes(0) if($no_write);
  
Jessica Severin's avatar
Jessica Severin committed
158 159 160 161 162 163 164
  return $worker;
}

sub register_worker_death {
  my ($self, $worker) = @_;

  return unless($worker);
Leo Gordon's avatar
Leo Gordon committed
165

Leo Gordon's avatar
bugfix  
Leo Gordon committed
166 167 168
  my $cod = $worker->cause_of_death();

  unless ($cod eq 'HIVE_OVERLOAD') {
169 170 171 172
    ## HIVE_OVERLOAD occurs after a successful update of the analysis_stats teble. (c.f. Worker.pm)
    $worker->analysis->stats->adaptor->decrease_running_workers($worker->analysis->stats->analysis_id);
  }

Jessica Severin's avatar
Jessica Severin committed
173
  my $sql = "UPDATE hive SET died=now(), last_check_in=now()";
174
  $sql .= " ,status='DEAD'";
Jessica Severin's avatar
Jessica Severin committed
175
  $sql .= " ,work_done='" . $worker->work_done . "'";
Leo Gordon's avatar
bugfix  
Leo Gordon committed
176
  $sql .= " ,cause_of_death='$cod'";
Leo Gordon's avatar
Leo Gordon committed
177
  $sql .= " WHERE worker_id='" . $worker->worker_id ."'";
Jessica Severin's avatar
Jessica Severin committed
178

Leo Gordon's avatar
bugfix  
Leo Gordon committed
179
  $self->dbc->do( $sql );
180

Leo Gordon's avatar
bugfix  
Leo Gordon committed
181
  if($cod eq 'NO_WORK') {
182
    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, 'ALL_CLAIMED');
183
  }
Leo Gordon's avatar
bugfix  
Leo Gordon committed
184 185 186 187
  if($cod eq 'FATALITY'
  or $cod eq 'MEMLIMIT'
  or $cod eq 'RUNLIMIT'
  or $cod eq 'KILLED_BY_USER') {
Leo Gordon's avatar
Leo Gordon committed
188
    $self->db->get_AnalysisJobAdaptor->release_undone_jobs_from_worker($worker);
189
  }
190
  
191
  # re-sync the analysis_stats when a worker dies as part of dynamic sync system
192
  if($self->safe_synchronize_AnalysisStats($worker->analysis->stats)->status ne 'DONE') {
193 194
    # since I'm dying I should make sure there is someone to take my place after I'm gone ...
    # above synch still sees me as a 'living worker' so I need to compensate for that
195
    $self->db->get_AnalysisStatsAdaptor->increase_needed_workers($worker->analysis->dbID);
196 197
  }

Jessica Severin's avatar
Jessica Severin committed
198 199
}

Leo Gordon's avatar
Leo Gordon committed
200 201 202
sub check_for_dead_workers {
    my ($self, $meadow, $check_buried_in_haste) = @_;

203
    my $worker_status_hash    = $meadow->status_of_all_our_workers();
Leo Gordon's avatar
Leo Gordon committed
204 205 206 207 208
    my %worker_status_summary = ();
    my $queen_worker_list     = $self->fetch_overdue_workers(0);

    print "====== Live workers according to    Queen:".scalar(@$queen_worker_list).", Meadow:".scalar(keys %$worker_status_hash)."\n";

209 210
    my %gc_wpid_to_worker = ();

Leo Gordon's avatar
Leo Gordon committed
211 212 213 214 215 216 217 218
    foreach my $worker (@$queen_worker_list) {
        next unless($meadow->responsible_for_worker($worker));

        my $worker_pid = $worker->process_id();
        if(my $status = $worker_status_hash->{$worker_pid}) { # can be RUN|PEND|xSUSP
            $worker_status_summary{$status}++;
        } else {
            $worker_status_summary{'AWOL'}++;
219

220
            $gc_wpid_to_worker{$worker_pid} = $worker;
Leo Gordon's avatar
Leo Gordon committed
221 222 223 224
        }
    }
    print "\t".join(', ', map { "$_:$worker_status_summary{$_}" } keys %worker_status_summary)."\n\n";

225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241
    if(my $total_lost = scalar(keys %gc_wpid_to_worker)) {
        warn "GarbageCollector: Discovered $total_lost lost workers\n";

        my $wpid_to_cod = {};
        if(UNIVERSAL::can($meadow, 'find_out_causes')) {
            $wpid_to_cod = $meadow->find_out_causes( keys %gc_wpid_to_worker );
            my $lost_with_known_cod = scalar(keys %$wpid_to_cod);
            warn "GarbageCollector: Found why $lost_with_known_cod of them died\n";
        }

        warn "GarbageCollector: Releasing the jobs\n";
        while(my ($worker_pid, $worker) = each %gc_wpid_to_worker) {
            $worker->cause_of_death( $wpid_to_cod->{$worker_pid} || 'FATALITY');
            $self->register_worker_death($worker);
        }
    }

Leo Gordon's avatar
Leo Gordon committed
242 243 244 245 246 247 248 249
    if($check_buried_in_haste) {
        print "====== Checking for workers buried in haste... ";
        my $buried_in_haste_list = $self->fetch_dead_workers_with_jobs();
        if(my $bih_number = scalar(@$buried_in_haste_list)) {
            print "$bih_number, reclaiming jobs.\n\n";
            if($bih_number) {
                my $job_adaptor = $self->db->get_AnalysisJobAdaptor();
                foreach my $worker (@$buried_in_haste_list) {
Leo Gordon's avatar
Leo Gordon committed
250
                    $job_adaptor->release_undone_jobs_from_worker($worker);
Leo Gordon's avatar
Leo Gordon committed
251 252 253 254 255 256 257
                }
            }
        } else {
            print "none\n";
        }
    }
}
Jessica Severin's avatar
Jessica Severin committed
258

259
sub worker_check_in {
Jessica Severin's avatar
Jessica Severin committed
260 261 262 263
  my ($self, $worker) = @_;

  return unless($worker);
  my $sql = "UPDATE hive SET last_check_in=now()";
264
  $sql .= " ,work_done='" . $worker->work_done . "'";
Leo Gordon's avatar
Leo Gordon committed
265
  $sql .= " WHERE worker_id='" . $worker->worker_id ."'";
Jessica Severin's avatar
Jessica Severin committed
266 267 268 269

  my $sth = $self->prepare($sql);
  $sth->execute();
  $sth->finish;
270
  
271
  $self->safe_synchronize_AnalysisStats($worker->analysis->stats);
Jessica Severin's avatar
Jessica Severin committed
272 273 274
}


275
=head2 reset_and_fetch_job_by_dbID
276 277 278

  Arg [1]: int $analysis_job_id
  Example: 
279
    my $job = $queen->reset_and_fetch_job_by_dbID($analysis_job_id);
280 281
  Description: 
    For the specified analysis_job_id it will fetch just that job, 
282 283 284
    reset it completely as if it has never run, and return it.  
    Specifying a specific job bypasses the safety checks, 
    thus multiple workers could be running the 
285 286
    same job simultaneously (use only for debugging).
  Returntype : 
287
    Bio::EnsEMBL::Hive::AnalysisJob object
288
  Exceptions :
289
  Caller     : beekeepers, runWorker.pl scripts
290 291 292

=cut

293 294
sub reset_and_fetch_job_by_dbID {
  my $self = shift;
295
  my $analysis_job_id = shift;
296
  
297
  my $jobDBA = $self->db->get_AnalysisJobAdaptor;
298 299 300 301 302
  $jobDBA->reset_job_by_dbID($analysis_job_id); 

  my $job = $jobDBA->fetch_by_dbID($analysis_job_id); 
  my $stats = $self->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($job->analysis_id);
  $self->synchronize_AnalysisStats($stats);
303
  
304 305 306 307 308 309 310 311 312 313
  return $job;
}


sub worker_reclaim_job {
  my $self   = shift;
  my $worker = shift;
  my $job    = shift;

  return undef unless($job and $worker);
Leo Gordon's avatar
Leo Gordon committed
314
  $job->worker_id($worker->worker_id);
315
  $self->db->get_AnalysisJobAdaptor->reclaim_job($job);
316 317 318 319 320 321 322 323 324 325
  return $job;
}


######################################
#
# Public API interface for beekeeper
#
######################################

326 327 328
    # Note: asking for Queen->fetch_overdue_workers(0) essentially means
    #       "fetch all workers known to the Queen not to be officially dead"
    #
329 330 331 332 333 334 335 336 337 338
sub fetch_overdue_workers {
  my ($self,$overdue_secs) = @_;

  $overdue_secs = 3600 unless(defined($overdue_secs));

  my $constraint = "h.cause_of_death='' ".
                   "AND (UNIX_TIMESTAMP()-UNIX_TIMESTAMP(h.last_check_in))>$overdue_secs";
  return $self->_generic_fetch($constraint);
}

339 340
sub fetch_failed_workers {
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
341

342 343 344 345
  my $constraint = "h.cause_of_death='FATALITY' ";
  return $self->_generic_fetch($constraint);
}

Leo Gordon's avatar
Leo Gordon committed
346 347 348
sub fetch_dead_workers_with_jobs {
  my $self = shift;

Leo Gordon's avatar
Leo Gordon committed
349
  # select h.worker_id from hive h, analysis_job WHERE h.worker_id=analysis_job.worker_id AND h.cause_of_death!='' AND analysis_job.status not in ('DONE', 'READY','FAILED') group by h.worker_id
Leo Gordon's avatar
Leo Gordon committed
350

Leo Gordon's avatar
bugfix  
Leo Gordon committed
351
  my $constraint = "h.cause_of_death!='' ";
Leo Gordon's avatar
Leo Gordon committed
352
  my $join = [[['analysis_job', 'j'], " h.worker_id=j.worker_id AND j.status NOT IN ('DONE', 'READY', 'FAILED') GROUP BY h.worker_id"]];
Leo Gordon's avatar
Leo Gordon committed
353 354
  return $self->_generic_fetch($constraint, $join);
}
Jessica Severin's avatar
Jessica Severin committed
355

356 357
=head2 synchronize_hive

Leo Gordon's avatar
Leo Gordon committed
358
  Arg [1]    : $filter_analysis (optional)
359 360 361 362 363 364 365 366 367 368 369
  Example    : $queen->synchronize_hive();
  Description: Runs through all analyses in the system and synchronizes
              the analysis_stats summary with the states in the analysis_job 
              and hive tables.  Then follows by checking all the blocking rules
              and blocks/unblocks analyses as needed.
  Exceptions : none
  Caller     : general

=cut

sub synchronize_hive {
Leo Gordon's avatar
Leo Gordon committed
370
  my $self          = shift;
Leo Gordon's avatar
Leo Gordon committed
371
  my $filter_analysis = shift; # optional parameter
372

373
  my $start_time = time();
374

Leo Gordon's avatar
Leo Gordon committed
375
  my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
376

Leo Gordon's avatar
Leo Gordon committed
377
  print STDERR "\nSynchronizing the hive (".scalar(@$list_of_analyses)." analyses this time):\n";
Leo Gordon's avatar
Leo Gordon committed
378 379
  foreach my $analysis (@$list_of_analyses) {
    $self->synchronize_AnalysisStats($analysis->stats);
Leo Gordon's avatar
Leo Gordon committed
380
    print STDERR '.';
381
  }
Leo Gordon's avatar
Leo Gordon committed
382
  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
383

Leo Gordon's avatar
Leo Gordon committed
384
  print STDERR "Checking blocking control rules:\n";
Leo Gordon's avatar
Leo Gordon committed
385
  foreach my $analysis (@$list_of_analyses) {
386
    $self->check_blocking_control_rules_for_AnalysisStats($analysis->stats);
Leo Gordon's avatar
Leo Gordon committed
387
    print STDERR '.';
388
  }
Leo Gordon's avatar
Leo Gordon committed
389
  print STDERR "\n";
Leo Gordon's avatar
Leo Gordon committed
390

Leo Gordon's avatar
Leo Gordon committed
391
  print STDERR ''.((time() - $start_time))." seconds to synchronize_hive\n\n";
392
}
393

394

395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416
=head2 safe_synchronize_AnalysisStats

  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
  Description: Prewrapper around synchronize_AnalysisStats that does
               checks and grabs sync_lock before proceeding with sync.
               Used by distributed worker sync system to avoid contention.
  Exceptions : none
  Caller     : general

=cut

sub safe_synchronize_AnalysisStats {
  my $self = shift;
  my $stats = shift;

  return $stats unless($stats);
  return $stats unless($stats->analysis_id);
  return $stats if($stats->status eq 'SYNCHING');
  return $stats if($stats->status eq 'DONE');
  return $stats if($stats->sync_lock);
  return $stats if(($stats->status eq 'WORKING') and
417
                   ($stats->seconds_since_last_update < 3*60));
418 419 420 421

  # OK try to claim the sync_lock
  my $sql = "UPDATE analysis_stats SET status='SYNCHING', sync_lock=1 ".
            "WHERE sync_lock=0 and analysis_id=" . $stats->analysis_id;
422
  #print("$sql\n");
423 424
  my $row_count = $self->dbc->do($sql);  
  return $stats unless($row_count == 1);
425
  #printf("got sync_lock on analysis_stats(%d)\n", $stats->analysis_id);
426 427 428
  
  #OK have the lock, go and do the sync
  $self->synchronize_AnalysisStats($stats);
429

430 431 432 433
  return $stats;
}


434
=head2 synchronize_AnalysisStats
435

436 437 438 439 440 441 442 443
  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
  Description: Queries the analysis_job and hive tables to get summary counts
               and rebuilds the AnalysisStats object.  Then updates the
               analysis_stats table with the new summary info
  Returntype : newly synced Bio::EnsEMBL::Hive::AnalysisStats object
  Exceptions : none
  Caller     : general
444

445
=cut
446

447
sub synchronize_AnalysisStats {
448
  my $self = shift;
449
  my $analysisStats = shift;
450

451
  return $analysisStats unless($analysisStats);
452
  return $analysisStats unless($analysisStats->analysis_id);
453
  
454
  $analysisStats->refresh(); ## Need to get the new hive_capacity for dynamic analyses
455 456 457 458 459 460
  $analysisStats->total_job_count(0);
  $analysisStats->unclaimed_job_count(0);
  $analysisStats->done_job_count(0);
  $analysisStats->failed_job_count(0);
  $analysisStats->num_required_workers(0);

461 462
  my $sql = "SELECT status, count(*), semaphore_count FROM analysis_job ".
            "WHERE analysis_id=? GROUP BY status, semaphore_count";
463 464 465
  my $sth = $self->prepare($sql);
  $sth->execute($analysisStats->analysis_id);

466 467
  my $hive_capacity = $analysisStats->hive_capacity;

468
  while (my ($status, $count, $semaphore_count)=$sth->fetchrow_array()) {
469
# print STDERR "$status - $count\n";
470 471 472 473

    my $total = $analysisStats->total_job_count();
    $analysisStats->total_job_count($total + $count);

474
    if(($status eq 'READY') and ($semaphore_count<=0)) {
475
      $analysisStats->unclaimed_job_count($count);
476 477 478 479 480 481 482 483 484
      my $numWorkers;
      if($analysisStats->batch_size > 0) {
        $numWorkers = POSIX::ceil($count / $analysisStats->batch_size);
      } else {
        my $job_msec = $analysisStats->avg_msec_per_job;
        $job_msec = 100 if($job_msec>0 and $job_msec<100);
        $numWorkers = POSIX::ceil(($count * $job_msec) / (3*60*1000)); 
        # guess num needed workers by total jobs / (num jobs a worker could do in 3 minutes)
      }
485
      $numWorkers=$count if($numWorkers==0);
486 487 488 489 490
      if($analysisStats->hive_capacity>0 and $numWorkers > $analysisStats->hive_capacity) {
        $numWorkers=$analysisStats->hive_capacity;
      }
      $analysisStats->num_required_workers($numWorkers);
    }
491 492
    if ($status eq 'DONE') { $analysisStats->done_job_count($count); }
    if ($status eq 'FAILED') { $analysisStats->failed_job_count($count); }
493 494
  }
  $sth->finish;
495

496
  $self->check_blocking_control_rules_for_AnalysisStats($analysisStats);
497

498 499 500
  if($analysisStats->status ne 'BLOCKED') {
    $analysisStats->determine_status();
  }
501

502 503 504 505
  #
  # adjust_stats_for_living_workers
  #
  
506
  if($analysisStats->hive_capacity > 0) {
507
    my $liveCount = $analysisStats->get_running_worker_count();
508 509 510 511 512 513 514 515

    my $numWorkers = $analysisStats->num_required_workers;

    my $capacityAdjust = ($numWorkers + $liveCount) - $analysisStats->hive_capacity;
    $numWorkers -= $capacityAdjust if($capacityAdjust > 0);
    $numWorkers=0 if($numWorkers<0);

    $analysisStats->num_required_workers($numWorkers);
516
  }
517

518
  $analysisStats->update;  #update and release sync_lock
519

520
  return $analysisStats;
521
}
522 523


524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546
sub check_blocking_control_rules_for_AnalysisStats
{
  my $self = shift;
  my $stats = shift;
  
  return unless($stats);

  #print("check ctrl on analysis ");  $stats->print_stats;
  my $ctrlRules = $self->db->get_AnalysisCtrlRuleAdaptor->
                  fetch_by_ctrled_analysis_id($stats->analysis_id);
  my $allRulesDone = 1;
  if(scalar @$ctrlRules > 0) {
    #print("HAS blocking_ctrl_rules to check\n");
    foreach my $ctrlrule (@{$ctrlRules}) {
      #use this method because the condition_analysis objects can be
      #network distributed to a different database so use it's adaptor to get
      #the AnalysisStats object
      #$ctrlrule->print_rule;
      my $condAnalysis = $ctrlrule->condition_analysis;
      my $condStats = $condAnalysis->stats if($condAnalysis);
      $allRulesDone = 0 unless($condStats and $condStats->status eq 'DONE');
      #print("  "); $condStats->print_stats;
    }
547

548 549 550
    if($allRulesDone) {
      if($stats->status eq 'BLOCKED') {
        #print("  UNBLOCK analysis : all conditions met\n");
551
        $stats->update_status('LOADING'); #trigger sync
552 553 554 555
      }
    } else {
      #print("  RE-BLOCK analysis : some conditions failed\n");
      $stats->update_status('BLOCKED');
556 557
    }
  }
558 559 560
}


Leo Gordon's avatar
Leo Gordon committed
561 562
sub get_num_failed_analyses {
  my ($self, $analysis) = @_;
563 564

  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
Leo Gordon's avatar
Leo Gordon committed
565
  my $failed_analyses = $statsDBA->fetch_by_statuses(['FAILED']);
566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587
  if ($analysis) {
    foreach my $this_failed_analysis (@$failed_analyses) {
      if ($this_failed_analysis->analysis_id == $analysis->dbID) {
        print "#########################################################\n",
            " Too many jobs failed for analysis ".$analysis->logic_name.". FAIL!!\n",
            "#########################################################\n\n";
        return 1;
      }
    }
    return 0;
  }

  if (@$failed_analyses) {
    print "##################################################\n",
        " Too many failed jobs. FAIL!!\n",
        "##################################################\n";
  }

  return scalar(@$failed_analyses);
}


588 589
sub get_hive_current_load {
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
590
  my $sql = "SELECT sum(1/analysis_stats.hive_capacity) FROM hive, analysis_stats ".
591 592
            "WHERE hive.analysis_id=analysis_stats.analysis_id and cause_of_death ='' ".
            "AND analysis_stats.hive_capacity>0";
593 594 595 596 597
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $load)=$sth->fetchrow_array();
  $sth->finish;
  $load=0 unless($load);
Leo Gordon's avatar
Leo Gordon committed
598
  print("current hive load = $load\n");
599 600 601 602
  return $load;
}


603 604 605 606 607 608 609 610
sub get_num_running_workers {
  my $self = shift;
  my $sql = "SELECT count(*) FROM hive WHERE cause_of_death =''";
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $runningCount)=$sth->fetchrow_array();
  $sth->finish;
  $runningCount=0 unless($runningCount);
Leo Gordon's avatar
Leo Gordon committed
611
  print("current hive num_running_workers = $runningCount\n");
612 613 614
  return $runningCount;
}

615 616 617
sub enter_status {
  my ($self, $worker, $status) = @_;

Leo Gordon's avatar
Leo Gordon committed
618
  $self->dbc->do("UPDATE hive SET status = '$status' WHERE worker_id = ".$worker->worker_id);
619 620
}

621 622
=head2 get_num_needed_workers

623
  Arg[1]     : Bio::EnsEMBL::Analysis object (optional)
624 625 626 627
  Example    : $count = $queen->get_num_needed_workers();
  Description: Runs through the analyses in the system which are waiting
               for workers to be created for them.  Calculates the maximum
               number of workers needed to fill the current needs of the system
628
               If Arg[1] is defined, does it only for the given analysis.
629
  Exceptions : none
630
  Caller     : beekeepers and other external processes
631 632 633

=cut

634
sub get_num_needed_workers {
Leo Gordon's avatar
Leo Gordon committed
635
  my ($self, $filter_analysis) = @_;
636

637
  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
Leo Gordon's avatar
Leo Gordon committed
638 639 640
  my $clearly_needed_analyses     = $statsDBA->fetch_by_needed_workers(undef,$self->{maximise_concurrency});
  my $potentially_needed_analyses = $statsDBA->fetch_by_statuses(['LOADING', 'BLOCKED']);
  my @all_analyses = (@$clearly_needed_analyses, @$potentially_needed_analyses);
641

Leo Gordon's avatar
Leo Gordon committed
642
  return 0 unless(@all_analyses);
643

Leo Gordon's avatar
Leo Gordon committed
644
  my $available_load = 1.0 - $self->get_hive_current_load();
645

Leo Gordon's avatar
Leo Gordon committed
646
  return 0 if($available_load <=0.0);
647

Leo Gordon's avatar
Leo Gordon committed
648 649
  my $total_workers = 0;
  my %rc2workers = ();
650

651 652
# FIXME: I have a feeling sometimes this method returns an incorrect value. Please doublecheck.

Leo Gordon's avatar
Leo Gordon committed
653 654
  foreach my $analysis_stats (@all_analyses) {
    next if (defined $filter_analysis && $filter_analysis->dbID != $analysis_stats->analysis_id);
655

Leo Gordon's avatar
Leo Gordon committed
656
        #digging deeper under the surface so need to sync
657 658 659 660 661 662 663
    if(($analysis_stats->status eq 'LOADING') or ($analysis_stats->status eq 'BLOCKED')) {
      $self->synchronize_AnalysisStats($analysis_stats);
    }

    next if($analysis_stats->status eq 'BLOCKED');
    next if($analysis_stats->num_required_workers == 0);

Leo Gordon's avatar
Leo Gordon committed
664
    my $workers_this_analysis = $analysis_stats->num_required_workers;
665

Leo Gordon's avatar
Leo Gordon committed
666 667 668 669 670 671 672 673
    if($analysis_stats->hive_capacity > 0) {   # if there is a limit, use it for cut-off
        my $limit_workers_this_analysis = int($available_load * $analysis_stats->hive_capacity);

        if($workers_this_analysis > $limit_workers_this_analysis) {
            $workers_this_analysis = $limit_workers_this_analysis;
        }

        $available_load -= 1.0*$workers_this_analysis/$analysis_stats->hive_capacity;
674
    }
Leo Gordon's avatar
Leo Gordon committed
675 676 677 678 679 680
    $total_workers += $workers_this_analysis;
    $rc2workers{$analysis_stats->rc_id} += $workers_this_analysis;
    $analysis_stats->print_stats();
    printf("  (%1.3f remaining-hive-load) use %3d workers of analysis_id=%d\n", $available_load, $workers_this_analysis, $analysis_stats->analysis_id);

    last if($available_load <= 0.0);
681
  }
682

Leo Gordon's avatar
Leo Gordon committed
683 684 685 686
  printf("need a total of $total_workers workers (availLoad=%1.5f)\n", $available_load);
  return ($total_workers, \%rc2workers);
}

Leo Gordon's avatar
Leo Gordon committed
687
sub get_needed_workers_resync_if_necessary {
Leo Gordon's avatar
Leo Gordon committed
688 689 690 691 692 693 694 695 696 697 698 699 700 701 702
    my ($self, $meadow, $analysis) = @_;

    my $load                     = $self->get_hive_current_load();
    my $running_count            = $self->get_num_running_workers();
    my ($needed_count, $rc_hash) = $self->get_num_needed_workers($analysis);

    if($load==0 and $needed_count==0 and $running_count==0) {
        print "*** nothing is running and nothing to do (according to analysis_stats) => perform a hard resync\n" ;

        $self->synchronize_hive($analysis);
        $self->check_for_dead_workers($meadow, 1);

        ($needed_count, $rc_hash) = $self->get_num_needed_workers($analysis);
    }

Leo Gordon's avatar
Leo Gordon committed
703
    return ($needed_count, $rc_hash);
704 705
}

Leo Gordon's avatar
Leo Gordon committed
706
sub get_remaining_jobs_show_hive_progress {
707
  my $self = shift;
Leo Gordon's avatar
Leo Gordon committed
708
  my $sql = "SELECT sum(done_job_count), sum(failed_job_count), sum(total_job_count), ".
709 710
            "sum(unclaimed_job_count * analysis_stats.avg_msec_per_job)/1000/60/60 ".
            "FROM analysis_stats";
711 712
  my $sth = $self->prepare($sql);
  $sth->execute();
713
  my ($done, $failed, $total, $cpuhrs) = $sth->fetchrow_array();
714
  $sth->finish;
715 716 717 718 719 720 721

  $done   ||= 0;
  $failed ||= 0;
  $total  ||= 0;
  my $completed = $total
    ? ((100.0 * ($done+$failed))/$total)
    : 0.0;
722 723 724
  my $remaining = $total - $done - $failed;
  printf("hive %1.3f%% complete (< %1.3f CPU_hrs) (%d todo + %d done + %d failed = %d total)\n", 
          $completed, $cpuhrs, $remaining, $done, $failed, $total);
Leo Gordon's avatar
Leo Gordon committed
725
  return $remaining;
726 727
}

728 729 730 731 732 733 734 735
## Can't see where this method is used.
#
#sub print_hive_status {
#    my ($self, $filter_analysis) = @_;
#
#    $self->print_analysis_status($filter_analysis);
#    $self->print_running_worker_status;
#}
736 737


Leo Gordon's avatar
Leo Gordon committed
738
sub print_analysis_status {
Leo Gordon's avatar
Leo Gordon committed
739
    my ($self, $filter_analysis) = @_;
740

Leo Gordon's avatar
Leo Gordon committed
741
    my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
Leo Gordon's avatar
Leo Gordon committed
742 743 744
    foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
        $analysis->stats->print_stats($self->{'verbose_stats'});
    }
745 746 747
}


Leo Gordon's avatar
Leo Gordon committed
748
sub print_running_worker_status {
749
  my $self = shift;
750

Leo Gordon's avatar
Leo Gordon committed
751
  print "====== Live workers according to Queen:\n";
752 753 754
  my $sql = "select logic_name, count(*) from hive, analysis ".
            "where hive.analysis_id=analysis.analysis_id and hive.cause_of_death='' ".
            "group by hive.analysis_id";
Leo Gordon's avatar
Leo Gordon committed
755 756

  my $total = 0;
757 758 759 760
  my $sth = $self->prepare($sql);
  $sth->execute();
  while((my $logic_name, my $count)=$sth->fetchrow_array()) {
    printf("%20s : %d workers\n", $logic_name, $count);
761
    $total += $count;
762
  }
763
  printf("  %d total workers\n", $total);
Leo Gordon's avatar
Leo Gordon committed
764
  print "===========================\n";
765
  $sth->finish;
766
}
767

768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796
=head2 monitor

  Arg[1]     : --none--
  Example    : $queen->monitor();
  Description: Monitors current throughput and store the result in the monitor
               table
  Exceptions : none
  Caller     : beekeepers and other external processes

=cut

sub monitor
{
  my $self = shift;
  my $sql = qq{
      INSERT INTO monitor
      SELECT
          now(),
          count(*),
          sum(work_done/TIME_TO_SEC(TIMEDIFF(now(),born))),
          sum(work_done/TIME_TO_SEC(TIMEDIFF(now(),born)))/count(*),
          group_concat(DISTINCT logic_name)
      FROM hive left join analysis USING (analysis_id)
      WHERE cause_of_death = ""};
      
  my $sth = $self->prepare($sql);
  $sth->execute();
}

Leo Gordon's avatar
Leo Gordon committed
797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814
=head2 register_all_workers_dead

  Example    : $queen->register_all_workers_dead();
  Description: Registers all workers dead
  Exceptions : none
  Caller     : beekeepers and other external processes

=cut

sub register_all_workers_dead {
    my $self = shift;

    my $overdueWorkers = $self->fetch_overdue_workers(0);
    foreach my $worker (@{$overdueWorkers}) {
        $self->register_worker_death($worker);
    }
}

815

Jessica Severin's avatar
Jessica Severin committed
816 817 818 819 820
#
# INTERNAL METHODS
#
###################

821
sub _pick_best_analysis_for_new_worker {
Leo Gordon's avatar
Leo Gordon committed
822 823
  my $self  = shift;
  my $rc_id = shift;    # this parameter will need to percolate very deep
824 825 826 827

  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
  return undef unless($statsDBA);

Leo Gordon's avatar
Leo Gordon committed
828
  my ($stats) = @{$statsDBA->fetch_by_needed_workers(1,$self->{maximise_concurrency}, $rc_id)};
829 830 831 832 833
  if($stats) {
    #synchronize and double check that it can be run
    $self->safe_synchronize_AnalysisStats($stats);
    return $stats if(($stats->status ne 'BLOCKED') and ($stats->num_required_workers > 0));
  }
834 835

  # ok so no analyses 'need' workers.
836 837 838
  if ($self->get_num_failed_analyses()) {
    return undef;
  }
839 840 841 842
  # see if anything needs an update, in case there are
  # hidden jobs that haven't made it into the summary stats

  print("QUEEN: no obvious needed workers, need to dig deeper\n");
Leo Gordon's avatar
Leo Gordon committed
843
  my $stats_list = $statsDBA->fetch_by_statuses(['LOADING', 'BLOCKED']);
844
  foreach $stats (@$stats_list) {
845
    $self->safe_synchronize_AnalysisStats($stats);
846

Leo Gordon's avatar
Leo Gordon committed
847
    return $stats if(($stats->status ne 'BLOCKED') and ($stats->num_required_workers > 0) and (!defined($rc_id) or ($stats->rc_id == $rc_id)));
848 849
  }

Leo Gordon's avatar
Leo Gordon committed
850
  ($stats) = @{$statsDBA->fetch_by_needed_workers(1,$self->{maximise_concurrency}, $rc_id)};
851 852 853 854 855 856
  return $stats if($stats);

  return undef;
}


Leo Gordon's avatar
Leo Gordon committed
857
=head2 fetch_by_worker_id
Jessica Severin's avatar
Jessica Severin committed
858 859 860

  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
861
  Example    : $feat = $queen->fetch_by_dbID(1234);
Jessica Severin's avatar
Jessica Severin committed
862 863 864 865 866 867 868 869
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Hive::Worker
  Exceptions : thrown if $id is not defined
  Caller     : general

=cut

Leo Gordon's avatar
Leo Gordon committed
870
sub fetch_by_worker_id {
Jessica Severin's avatar
Jessica Severin committed
871 872 873
  my ($self,$id) = @_;

  unless(defined $id) {
874
    throw("fetch_by_dbID must have an id");
Jessica Severin's avatar
Jessica Severin committed
875 876 877 878
  }

  my @tabs = $self->_tables;

Leo Gordon's avatar
Leo Gordon committed
879
  my $constraint = "h.worker_id = $id";
Jessica Severin's avatar
Jessica Severin committed
880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962

  #return first element of _generic_fetch list
  my ($obj) = @{$self->_generic_fetch($constraint)};
  return $obj;
}

=head2 _generic_fetch

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch

=cut

sub _generic_fetch {
  my ($self, $constraint, $join) = @_;

  my @tables = $self->_tables;
  my $columns = join(', ', $self->_columns());

  if ($join) {
    foreach my $single_join (@{$join}) {
      my ($tablename, $condition, $extra_columns) = @{$single_join};
      if ($tablename && $condition) {
        push @tables, $tablename;

        if($constraint) {
          $constraint .= " AND $condition";
        } else {
          $constraint = " $condition";
        }
      }
      if ($extra_columns) {
        $columns .= ", " . join(', ', @{$extra_columns});
      }
    }
  }

  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql = "SELECT $columns FROM $tablenames";

  my $default_where = $self->_default_where_clause;
  my $final_clause = $self->_final_clause;

  #append a where clause if it was defined
  if($constraint) {
    $sql .= " WHERE $constraint ";
    if($default_where) {
      $sql .= " AND $default_where ";
    }
  } elsif($default_where) {
    $sql .= " WHERE $default_where ";
  }